chr4-141256726-A-T

Variant names:

• chr4-141256726-A-T
• rs1541964
• ENST00000514347.1:n.447-15397T>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000514347.1(ENSG00000248747):​n.447-15397T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 152,088 control chromosomes in the GnomAD database, including 39,727 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.71 (39727 hom., cov: 32)
• Consequence: ENSG00000248747 ENST00000514347.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297

Genes affected

ENSG00000248747 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248747	ENST00000514347.1	n.447-15397T>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107527 AN: 151970 Hom.: 39671 Cov.: 32

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.708

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.708 AC: 107643 AN: 152088 Hom.: 39727 Cov.: 32 AF XY: 0.703 AC XY: 52220 AN XY: 74330

Gnomad4 AFR AF: 0.923

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.781

Gnomad4 SAS AF: 0.762

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.612

Gnomad4 OTH AF: 0.704

Alfa AF: 0.649 Hom.: 3886

Bravo AF: 0.725

Asia WGS AF: 0.753 AC: 2610 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.32

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1541964; hg19: chr4-142177880;